Detection of novel orthonairovirus and unclassified flavivirus in Rhipicephalus appendiculatus ticks in Kenya

Tick-borne viruses (TBVs) include the highly pathogenic viruses associated with infectious diseases in both humans and animals. The global public health concern of TBVs is closely related to geographic distribution of ticks. In Africa, a variety of TBVs have been reported by detections from ticks and high seroprevalence in humans and domestic animals. In this study, we aimed to detect TBVs from ticks in Kenya by targeting viral genes of Orthoflavivirus, Bandavirus and Orthonairovirus. Ticks were collected from cattle, camels, sheep and goats in Isiolo, Narok and Baringo counties, and viral RNA detections were attempted by RT-PCR. There were no positive samples for Orthoflavivirus and Bandavirus. On the other hand, 10 samples tested positive for Orthonairovirus by RT-PCR, were identified from Rhipicephalus appendiculatus tick pools. Five pools were indicated as novel Orthonairovirus species, marigat tick orthonairovirus (MTOV). Interestingly, other 5 samples were considered to be Bole tick virus 4 (BLTV4) and BLTV4-related virus, marigat tick flavivirus (MTFV), belonging to unclassified genus within family Flaviviridae, but not Orthonairovirus. Our findings add to the knowledge of genetic diversity and geographic distribution of tick-borne viruses including novel Orthonairovirus MTOV, unclassified Flavivirus BLTV4 and MTFV in Kenya, and will provide useful clues for further epidemiological surveys.